Package: DAISIE 4.5.0

DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.

Authors:Rampal S. Etienne [aut, cre], Luis Valente [aut], Albert B. Phillimore [aut], Bart Haegeman [aut], Joshua W. Lambert [aut], Pedro Santos Neves [aut], Shu Xie [aut], Richèl J.C. Bilderbeek [aut], Hanno Hildenbrandt [aut], Torsten Hauffe [ctb], Giovanni Laudanno [ctb], Nadiah Kristensen [ctb], Raphael Scherrer [ctb]

DAISIE_4.5.0.tar.gz
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DAISIE.pdf |DAISIE.html
DAISIE/json (API)
NEWS

# Install 'DAISIE' in R:
install.packages('DAISIE', repos = c('https://rsetienne.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rsetienne/daisie/issues21 issues

Pkgdown site:https://rsetienne.github.io

Uses libs:
  • fortran– Runtime library for GNU Fortran applications
  • c++– GNU Standard C++ Library v3
Datasets:
  • Bats_GreaterAntilles - Colonization and branching times of Noctilionoid bats from the Greater Antilles.
  • Biwa_datalist - Colonization and branching times of 68 fish clades.
  • Galapagos_datalist - Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all
  • Galapagos_datalist_2types - Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_all
  • Galapagos_datatable - Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table format.
  • Macaronesia_datalist - Colonization and branching times of terrestrial avifaunal clades from Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by DAISIE_ML and DAISIE_loglik_all
  • NewZealand_birds_datalist - Colonization and branching times of New Zealand birds.
  • archipelago_data - Physical data on 41 archipelagos
  • archipelagos41 - DAISIE datalist object including bird phylogenetic data and physical data for 41 archipelagos
  • frogs_datalist - Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island.
  • frogs_datatable - Colonization and branching times of 5 Eleutherodactylus (frogs) clades from the island of Hispaniola.
  • frogs_sim_datalist - Colonization and branching times of a data set simulated with the MLE parameters of frogs_datalist
  • islands_10reps_RAW - 1000 islands in RAW format simulated with the ML parameters of the CR model for the Galapagos data.
  • islands_1type_1000reps - 1000 islands in DAISIE format simulated with the ML parameters of the CR model for the Galapagos data
  • islands_2types_1000reps - 1000 islands in DAISIE format simulated with the ML parameters of the CR_lamc_mu_K model for the Galapagos data
  • stac_table - Explanatory table on meaning and use of 'stac' settings

On CRAN:DAISIE-4.5.0(2025-02-05)

fortrancpp

8.59 score 9 stars 1 packages 55 scripts 273 downloads 5 mentions 43 exports 44 dependencies

Last updated 18 days agofrom:48b6fb585f. Checks:9 OK, 2 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 05 2025
R-4.5-win-x86_64OKFeb 05 2025
R-4.5-mac-x86_64OKFeb 05 2025
R-4.5-mac-aarch64OKFeb 05 2025
R-4.5-linux-x86_64OKFeb 05 2025
R-4.4-win-x86_64NOTEFeb 05 2025
R-4.4-mac-x86_64OKFeb 05 2025
R-4.4-mac-aarch64OKFeb 05 2025
R-4.3-win-x86_64NOTEFeb 05 2025
R-4.3-mac-x86_64OKFeb 05 2025
R-4.3-mac-aarch64OKFeb 05 2025

Exports:create_area_parscreate_CS_versioncreate_hyper_parscreate_parscreate_trait_parscreate_trait_pars_2KDAISIE_abm_factorDAISIE_convertprobdistDAISIE_count_speciesDAISIE_CS_max_stepsDAISIE_dataprepDAISIE_ExpEINDAISIE_ICDAISIE_IW_num_threadsDAISIE_loglik_allDAISIE_loglik_CSDAISIE_loglik_IWDAISIE_logp0DAISIE_margprobdistDAISIE_MLDAISIE_ML_CSDAISIE_ML_IWDAISIE_MW_MLDAISIE_numcoldaisie_odeint_csdaisie_odeint_iwDAISIE_plot_age_diversityDAISIE_plot_inputDAISIE_plot_islandDAISIE_plot_simsDAISIE_probdistDAISIE_simDAISIE_sim_crDAISIE_sim_cr_shiftDAISIE_sim_MWDAISIE_sim_relaxed_rateDAISIE_sim_time_depDAISIE_sim_trait_depDAISIE_sim_trait_dep_2KDAISIE_SR_loglik_allDAISIE_SR_loglik_CSDAISIE_SR_MLDAISIE_SR_ML_CS

Dependencies:apeBHcliclusterGenerationcodacodetoolscombinatcpp11DDDDEoptimdeSolvedigestdoParallelexpmfastmatchforeachgenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtnlmenumDerivoptimParallelphangornphytoolspkgconfigpracmaquadprogRcppRcppEigenrlangscatterplot3dSparseMsubplextensortestitvctrs

DAISIE stac values

Rendered fromstac_key.Rmdusingknitr::rmarkdownon Feb 05 2025.

Last update: 2022-04-14
Started: 2022-04-14

DAISIE FAQs

Rendered fromDAISIE_FAQs.Rmdusingknitr::rmarkdownon Feb 05 2025.

Last update: 2025-02-05
Started: 2025-01-30

Demo optimizing parameters

Rendered fromdemo_optimize.Rmdusingknitr::rmarkdownon Feb 05 2025.

Last update: 2021-05-26
Started: 2019-03-19

Demo simulating islands

Rendered fromdemo_sim.Rmdusingknitr::rmarkdownon Feb 05 2025.

Last update: 2022-04-14
Started: 2019-03-19

Demo: Fitting clade-specific and island-wide diversity-dependence models in DAISIE

Rendered fromdemo_CSvsIW.Rmdusingknitr::rmarkdownon Feb 05 2025.

Last update: 2022-04-14
Started: 2020-08-11

Citation

To cite package ‘DAISIE’ in publications use:

Etienne R, Valente L, Phillimore A, Haegeman B, Lambert J, Santos Neves P, Xie S, Bilderbeek R, Hildenbrandt H (2025). DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction. R package version 4.5.0, , https://github.com/rsetienne/daisie.

Corresponding BibTeX entry:

  @Manual{,
    title = {DAISIE: Dynamical Assembly of Islands by Speciation,
      Immigration and Extinction},
    author = {Rampal S. Etienne and Luis Valente and Albert B.
      Phillimore and Bart Haegeman and Joshua W. Lambert and Pedro
      {Santos Neves} and Shu Xie and Richèl J.C. Bilderbeek and Hanno
      Hildenbrandt},
    year = {2025},
    note = {R package version 4.5.0, },
    url = {https://github.com/rsetienne/daisie},
  }

Readme and manuals

DAISIE: Dynamic Assembly of Island biota through Speciation, Immigration and Extinction

Branch GHA logo Codecov logo
master R build status codecov.io
develop R build status codecov.io

DAISIE is an R package that simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction.

The model can be fitted to both empirical dated phylogenies and simulated data.

  • For an overview of the simulation functionality see here.
  • Details and an overview of the maximum likelihood inference capabilities to estimate parameters see here.
  • For details on comparing between two diversity dependence models see here.

Installing DAISIE

N.B.: MacOS users may experience issues when installing DAISIE, especially when on MacOS Big Sur. If that is you case, please see here for detailed installation instructions.

The DAISIE package has a stable version on CRAN and a development version on GitHub.

From CRAN

From within R, do:

install.packages("DAISIE")
From GitHub

Install DAISIE from this GitHub repository by running:

install.packages("remotes")
# remotes::install_github("rsetienne/DAISIE")
install.packages("DAISIE", repos = c('https://rsetienne.r-universe.dev', 'https://cloud.r-project.org'))

Using DAISIE as a package dependency

From CRAN

To your DESCRIPTION file, add DAISIE as any normal package.

If your package directly uses DAISIE:

Imports:
  DAISIE

If your package uses DAISIE in its peripherals (e.g. vignettes and tests):

Suggests:
  DAISIE
From GitHub
Remotes:
  rsetienne/DAISIE

Support/Questions

For feature requests or bug-reports or other matters, please submit an issue.

Feature branches

  • master: build should always pass. @rsetienne has control over develop to master merges.
  • develop: merge of feature branches, merge with master by @rsetienne iff build passes.

Contributors

DAISIE was originally developed by Rampal S. Etienne, Luis Valente, Albert B. Phillimore and Bart Haegeman. It is continuously maintained by members of the @tece-lab, at the University of Groningen.

References

  • Etienne R. S., Valente, L., Phillimore, A. B., Haegeman, B., Lambert, J. W., Neves, P., Xie, S., Bilderbeek, R. J. C., & Hildenbrandt, H. (2021). DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction. R package version 4.0.2. https://cran.r-project.org/package=DAISIE. https://doi.org/10.5281/zenodo.4054058

  • Valente, L., Etienne, R.S., & Phillimore, A.B. (2014). The effects of island ontogeny on species diversity and phylogeny. Proceedings of the Royal Society B: Biological Sciences, 281(1784), 20133227–20133227. http://doi.org/10.1098/rspb.2013.3227

  • Valente, L., Phillimore, A.B., & Etienne, R.S. (2015). Equilibrium and non-equilibrium dynamics simultaneously operate in the Galápagos islands. Ecology Letters, 18(8), 844–852. http://doi.org/10.1111/ele.12461

  • Valente, L., Etienne, R.S., & Dávalos, L.M. (2017). Recent extinctions disturb path to equilibrium diversity in Caribbean bats. Nature Ecology & Evolution, 1(2), 0026. http://doi.org/10.1038/s41559-016-0026

  • Valente, L., Illera, J.C., Havenstein, K., Pallien, T., Etienne, R.S., & Tiedemann, R. (2017). Equilibrium Bird Species Diversity in Atlantic Islands. Current Biology, 27(11), 1660-1666. https://doi.org/10.1016/j.cub.2017.04.053

  • Valente, L., Phillimore, A.B., & Etienne, R.S. (2018). Using molecular phylogenies in island biogeography: It’s about time. Ecography, 1–3. http://doi.org/10.1111/ecog.03503

  • Valente, L., Etienne, R.S., & Garcia-R., J.C. (2019). Deep Macroevolutionary Impact of Humans on New Zealand’s Unique Avifauna. Current Biology 29 (15): 2563-2569.e4. https://doi.org/10.1016/j.cub.2019.06.058

  • Valente, L., Phillimore, A.B., Melo, M., Warren, B.H., Clegg, S.M., Havenstein, K., Tiedemann, R., Illera, J.C., Thebaud, C., Aschenbach, T. & Etienne, R.S. (2020). A Simple Dynamic Model Explains the Diversity of Island Birds Worldwide. Nature 579 (7797): 92–96. https://doi.org/10.1038/s41586-020-2022-5

  • Hauffe, T., Delicado, D., Etienne, R.S., & Valente, L. (2020). Lake expansion elevates equilibrium diversity via increasing colonization. Journal of Biogeography 47: 1849–1860. https://doi.org/10.1111/jbi.13914

  • Valente, L., Kristensen, N., Phillimore, A. B., & Etienne, R. S. (2021). Report of programming bugs in the DAISIE R package: consequences and correction. https://doi.org/10.32942/osf.io/w5ntf

  • Santos Neves, P.*, Lambert, J. W.*, Valente, L., & Etienne, R. S. (2022). The robustness of a simple dynamic model of island biodiversity to geological and sea-level change. Journal of Biogeography 49: 2091-2104. https://doi.org/10.1111/jbi.14519

  • Lambert, J. W., Santos Neves, P., Bilderbeek, R. L. C., Valente, L., Etienne, R. S. (2022). The effect of mainland dynamics on data and parameter estimates in island biogeography. bioRxiv. https://doi.org/10.1101/2022.01.13.476210

  • Xie, S., Valente, L., Etienne, R. S. (2023). Can we ignore trait-dependent colonization and diversification in island biogeography? Evolution. https://doi.org/10.1093/evolut/qpad006

  • Michielsen, N. M., Goodman, S. M., Soarimalala, V., van der Geer, A. A. E., Dávalos, L. M., Saville, G. I., Upham, N., Valente, L. (2023). The macroevolutionary impact of recent and imminent mammal extinctions on Madagascar. Nature Communications 14 (14). https://doi.org/10.1038/s41467-022-35215-3

Help Manual

Help pageTopics
Add a column to a data frameadd_column_to_dataframe
Physical data on 41 archipelagosarchipelago_data
DAISIE datalist object including bird phylogenetic data and physical data for 41 archipelagosarchipelagos41
Colonization and branching times of Noctilionoid bats from the Greater Antilles.Bats_GreaterAntilles
Colonization and branching times of 68 fish clades.Biwa_datalist
Create named list of area parameterscreate_area_pars
Creates the list object for CS_version argument in DAISIE_ML_CScreate_CS_version
Create list of hyperparameterscreate_hyper_pars
Create vector of model parameterscreate_pars
Create named list of trait state parameterscreate_trait_pars
Create named list of trait state parameterscreate_trait_pars_2K
Sets or retrieves the factor to calculate the step-size used by the odeint::adams_bashforth[_moulton] solvers.DAISIE_abm_factor
Converts the joint distribution of endemics and non-endemics under the DAISIE model to list formatDAISIE_convertprobdist
Count number of species in DAISIE datalist or simulated data.DAISIE_count_species
CS iteration controlDAISIE_CS_max_steps
Prepare colonisation and branching time data to run in DAISIE.DAISIE_dataprep
The expected number of endemics and non-endemics under the DAISIE modelDAISIE_ExpEIN
Formats clade-specific simulation output into standard DAISIE list output with complete STT tableDAISIE_format_CS_full_stt
Formats clade-specific simulation output into standard DAISIE list output with complete STT tableDAISIE_format_IW_full_stt
Calculates information criterion from DAISIE ML estimates?DAISIE_IC
IW concurrency controlDAISIE_IW_num_threads
Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parametersDAISIE_loglik_IW
The marginal distribution of endemics and non-endemics under the DAISIE modelDAISIE_margprobdist
Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependenceDAISIE_ML DAISIE_ML_CS
Maximization of the loglikelihood under the DAISIE model with island-wide diversity-dependenceDAISIE_ML_IW
Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependence and explicit dependencies on island area and isolation as hypothesized by MacArthur & WilsonDAISIE_MW_ML
The expectation and marginal distribution of the number of colonizations (lineages) under the DAISIE modelDAISIE_numcol
Driver for the boost::odeint solver for the CS modeldaisie_odeint_cs
Driver for the boost::odeint solver for the IW modeldaisie_odeint_iw
Plot clade age against clade diversity.DAISIE_plot_age_diversity
DAISIE tree plotDAISIE_plot_input
Plot colonisation and branching time of species found on an island dataset.DAISIE_plot_island
Plot island species-through-time (STT) plotsDAISIE_plot_sims
The joint distribution of endemics and non-endemics under the DAISIE modelDAISIE_probdist
Simulate (non-)oceanic islands with given parameters under time-constant ratesDAISIE_sim DAISIE_sim_cr
Simulates island replicates with an clade-specific (CS) diversity-dependent constant-rate processDAISIE_sim_cr_cs
Simulates island replicates with an guild-wide (GW) diversity-dependent processDAISIE_sim_cr_gw
Simulates island replicates with an island-wide (IW) diversity-dependent constant-rate processDAISIE_sim_cr_iw
Simulate (non-)oceanic islands with given parameters under a rate-shift regimeDAISIE_sim_cr_shift
Simulate multiple islands based on hyperparameters that describe relationships between area, isolation and local parametersDAISIE_sim_MW
Simulate (non-)oceanic islands with given parameters under a relaxed-rate modelDAISIE_sim_relaxed_rate
Simulate (non-)oceanic islands with given parameters under a time-dependent regimeDAISIE_sim_time_dep
Simulates island replicates with an clade-specific (CS) diversity-dependent time-dependent processDAISIE_sim_time_dep_cs
Simulates island replicates with an guild-wide (GW) diversity-dependent time-dependent processDAISIE_sim_time_dep_gw
Simulates island replicates with an island-wide (IW) diversity-dependent time-dependent processDAISIE_sim_time_dep_iw
Simulate islands with given trait-dependent parameters.DAISIE_sim_trait_dep
Simulate islands with given trait-dependent parameters.DAISIE_sim_trait_dep_2K
Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given data and a set of model parameters that may shift at some timeDAISIE_SR_loglik_all DAISIE_SR_loglik_CS
Maximization of the loglikelihood under the DAISIE model with clade-specific diversity-dependenceDAISIE_SR_ML DAISIE_SR_ML_CS
Colonization and branching times of 5 Eleutherodactylus clades from Hispaniola island.frogs_datalist
Colonization and branching times of 5 Eleutherodactylus (frogs) clades from the island of Hispaniola.frogs_datatable
Colonization and branching times of a data set simulated with the MLE parameters of frogs_datalistfrogs_sim_datalist
Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_allGalapagos_datalist
Colonization and branching times of 8 terrestrial avifaunal clades in list format, accepted by DAISIE_ML and DAISIE_loglik_allGalapagos_datalist_2types
Colonization and branching times of 8 terrestrial avifaunal Galápagos clades in table format.Galapagos_datatable
1000 islands in RAW format simulated with the ML parameters of the CR model for the Galapagos data.islands_10reps_RAW
1000 islands in DAISIE format simulated with the ML parameters of the CR model for the Galapagos dataislands_1type_1000reps
1000 islands in DAISIE format simulated with the ML parameters of the CR_lamc_mu_K model for the Galapagos data (2 types of species)islands_2types_1000reps
Colonization and branching times of terrestrial avifaunal clades from Azores, Canary Islands, Cape Verde and Madeira in list format, accepted by DAISIE_ML and DAISIE_loglik_allMacaronesia_datalist
Colonization and branching times of New Zealand birds.NewZealand_birds_datalist
Explanatory table on meaning and use of 'stac' settingsstac_table